FB2024_03 , released June 25, 2024
Gene: Dmel\Rab3GAP1
Open Close
General Information
Symbol
Dmel\Rab3GAP1
Species
D. melanogaster
Name
RAB3 GTPase activating protein subunit 1
Annotation Symbol
CG31935
Feature Type
protein_coding_gene
FlyBase ID
FBgn0051935
Gene Model Status
Current
Stock Availability
15 publicly available
Gene Summary
Catalytic subunit of the Rab3 GTPase-activating (Rab3GAP) complex composed of Rab3-GAP and Rab3GAP1, which has both GTPase-activating protein (GAP) activity towards Rab3, and guanine nucleotide exchange factor (GEF) activity towards Rab18 (Probable). As part of the Rab3GAP complex, required for the rapid induction and sustained expression of synaptic homeostasis at the neuromuscular junction (NMJ) (Probable). Also participates in the regulation of autophagy in tissues such as larval fat cells and adult muscles (Probable). The Rab3GAP complex, acts as a GAP for Rab3 by converting active Rab3-GTP to the inactive form Rab3-GDP (By similarity). At the neuromuscular junction (NMJ), forms a presynaptic signaling mechanism with Rab3 that regulates progression of synaptic homeostasis at a late stage of vesicle release (Probable). Within this mechanism Rab3-GTP acts, directly or indirectly, to inhibit the progression of synaptic homeostasis, and Rab3-GAP functions to inactivate this action of Rab3-GTP (Probable). The Rab3GAP complex, acts as a GEF for Rab18 by promoting the conversion of inactive Rab18-GDP to the active form Rab18-GTP (By similarity). Regulates autophagy as part of a Rab3GAP-Rab18 module (PubMed:32248620). Once Rab18 is activated by the GEF Rab3GAP complex, the Rab3GAP-Rab18 module localizes to autophagosomes, and regulates autolysosome formation and maturation together with the Rab18 interacting effector, the PI3K/Vps34 Complex I (PubMed:32248620). (UniProt, Q9VQ26)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
22A3-22A3
Sequence location
Recombination map
2-3
RefSeq locus
NT_033779 REGION:1594822..1611157
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables GTPase activator activity
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000484253
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with HGNC:17063
(Bernards, 2003)
inferred from electronic annotation with InterPro:IPR045700
(InterPro Project Members, 2004-)
enables small GTPase binding
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
Biological Process (10 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in macroautophagy
inferred from mutant phenotype
(Takáts et al., 2021)
Terms Based on Predictions or Assertions (9 terms)
CV Term
Evidence
References
involved_in establishment of protein localization to endoplasmic reticulum membrane
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
involved_in excitatory postsynaptic potential
inferred from sequence or structural similarity with UniProtKB:Q80UJ7
(Gene Ontology Curators, 2002-)
involved_in lipid droplet organization
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
involved_in positive regulation of endoplasmic reticulum tubular network organization
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
involved_in positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization
inferred from sequence or structural similarity with UniProtKB:Q80UJ7
(Gene Ontology Curators, 2002-)
involved_in positive regulation of GTPase activity
inferred from sequence or structural similarity with UniProtKB:Q80UJ7
(Gene Ontology Curators, 2002-)
involved_in regulation of calcium ion-dependent exocytosis of neurotransmitter
inferred from sequence or structural similarity with UniProtKB:Q80UJ7
(Gene Ontology Curators, 2002-)
involved_in regulation of Rab protein signal transduction
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
involved_in regulation of short-term neuronal synaptic plasticity
inferred from sequence or structural similarity with UniProtKB:Q80UJ7
(Gene Ontology Curators, 2002-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
located_in endoplasmic reticulum tubular network
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
part_of protein-containing complex
inferred from sequence or structural similarity with UniProtKB:Q15042
(Gene Ontology Curators, 2002-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the Rab3-GAP catalytic subunit family. (Q9VQ26)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
RAB GTPASE ACTIVATING PROTEINS -
RabGAPs are GTPase activating proteins for Rab family GTPases. RabGAPs share a common TBC (Tre-2/Bub2/Cdc16) domain. (Adapted from PMID:15731001 and FBrf0158741).
Protein Function (UniProtKB)
Catalytic subunit of the Rab3 GTPase-activating (Rab3GAP) complex composed of Rab3-GAP and Rab3GAP1, which has both GTPase-activating protein (GAP) activity towards Rab3, and guanine nucleotide exchange factor (GEF) activity towards Rab18 (Probable). As part of the Rab3GAP complex, required for the rapid induction and sustained expression of synaptic homeostasis at the neuromuscular junction (NMJ) (Probable). Also participates in the regulation of autophagy in tissues such as larval fat cells and adult muscles (Probable). The Rab3GAP complex, acts as a GAP for Rab3 by converting active Rab3-GTP to the inactive form Rab3-GDP (By similarity). At the neuromuscular junction (NMJ), forms a presynaptic signaling mechanism with Rab3 that regulates progression of synaptic homeostasis at a late stage of vesicle release (Probable). Within this mechanism Rab3-GTP acts, directly or indirectly, to inhibit the progression of synaptic homeostasis, and Rab3-GAP functions to inactivate this action of Rab3-GTP (Probable). The Rab3GAP complex, acts as a GEF for Rab18 by promoting the conversion of inactive Rab18-GDP to the active form Rab18-GTP (By similarity). Regulates autophagy as part of a Rab3GAP-Rab18 module (PubMed:32248620). Once Rab18 is activated by the GEF Rab3GAP complex, the Rab3GAP-Rab18 module localizes to autophagosomes, and regulates autolysosome formation and maturation together with the Rab18 interacting effector, the PI3K/Vps34 Complex I (PubMed:32248620).
(UniProt, Q9VQ26)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Rab3GAP1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VQ26)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.42

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Rodriguez et al., 2012, Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Rab3GAP1-RA
FBtr0077916
NM_134764
3058
916
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Rab3GAP1-PA
FBpp0077582
104.4
916
4.81
Q9VQ26
NP_608608
AAF51356
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

The Rab3 GTPase-activating complex is a heterodimer composed of Rab3GAP1 and Rab3-GAP.

(UniProt, Q9VQ26)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rab3GAP1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

1.28

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rab3GAP1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rab3GAP1
Transgenic constructs containing regulatory region of Rab3GAP1
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel6005
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\RAB3GAP1
14 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Rab3gap1
11 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Rab3gap1
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\rab3gap1
11 of 13
Yes
Yes
Xtro\ehd1
1 of 13
No
No
Danio rerio (Zebrafish) (1)
Drer\rab3gap1
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\rbg-1
12 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (0)
Arabidopsis thaliana (thale-cress) (2)
Atha\AT5G58510
12 of 13
Yes
Yes
Atha\AT5G55060
8 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Rab3GAP1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 2 )
    Potential Models Based on Orthology ( 1 )
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    RAB3GAP1; RAB3 GTPase activating protein catalytic subunit 1
    14 of 14
    602536
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Rab3GAP1 - Rab18
    pull down, peptide massfingerprinting
    (Gillingham et al., 2014)
    Rab3GAP1 - Rab5
    pull down, peptide massfingerprinting
    (Gillingham et al., 2014)
    Summary of Genetic Interactions
    esyN Network Diagram
    Other Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    The Rab3 GTPase-activating complex is a heterodimer composed of Rab3GAP1 and Rab3-GAP.
    (UniProt, Q9VQ26 )
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-3
    Cytogenetic map
    22A3-22A3
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    22A3-22A3
    Limits computationally determined from genome sequence between P{PZ}l(2)1068510685&P{lacW}Tango14k00619 and P{lacW}RFeSPk11704
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-3

    (FlyBase, 2016)

    2-2.7

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (15)
    Genomic Clones (32)
    cDNA Clones (1)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
      Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

          cDNA Clones, End Sequenced (ESTs)
          BDGP DGC clones
            Other clones
              RNAi and Array Information
              Linkouts
              DRSC - Results frm RNAi screens
              Antibody Information
              Laboratory Generated Antibodies
               
              Commercially Available Antibodies
               
              Cell Line Information
              Publicly Available Cell Lines
               
                Other Stable Cell Lines
                 
                  Other Comments
                  Relationship to Other Genes
                  Source for database merge of

                  Source for merge of: CG10870 CG7373

                  (FlyBase Genome Annotators, 2002-2003)
                  Additional comments

                  Annotations CG10870 and CG7373 merged as CG31935 in release 3 of the genome annotation.

                  (FlyBase Genome Annotators, 2002-2003)
                  Nomenclature History
                  Source for database identify of

                  Source for identity of: Rab3GAP1 CG31935

                  (Takáts et al., 2021)
                  Nomenclature comments
                  Etymology

                  The gene is named 'Rab3GAP1' based on orthology to human Rab3GAP1.

                  (Takáts et al., 2021)
                  Synonyms and Secondary IDs (6)
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  External Crossreferences and Linkouts ( 33 )
                  Sequence Crossreferences
                  NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
                  GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
                  GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
                  RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
                  UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
                  UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                  UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                  Other crossreferences
                  AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
                  DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                  EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                  FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                  FlyMine - An integrated database for Drosophila genomics
                  InterPro - A database of protein families, domains and functional sites
                  KEGG Genes - Molecular building blocks of life in the genomic space.
                  MARRVEL_MODEL - MARRVEL (model organism gene)
                  Linkouts
                  DroID - A comprehensive database of gene and protein interactions.
                  DRSC - Results frm RNAi screens
                  Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                  FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                  FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                  Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                  Flygut - An atlas of the Drosophila adult midgut
                  FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                  iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                  MIST (protein-protein) - An integrated Molecular Interaction Database
                  Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                  References (45)